Two things I meant to say:

Since the perl program now returns text according to your C program's definition, you won't have problems with popen

iso-8859-1 can only represent a small subset of the characters supported by UTF-16. The conversion to iso-8559-1 may result in information loss.

I don't know how I missed that the first time you posted it.

This is the first time I posted this. I needed to know what kind of data you had before I could post a solution. The solution is not a general solution. It would be inappropriate for XML, for example.